tar xvfz circos-0.69-9.tgzcd ~/Applications/circos-0.69-9/bin
./circos -modules
ok 1.29 Carp
ok 0.36 Clone
ok 2.63 Config::General
ok 3.40 Cwd
ok 2.145 Data::Dumper
ok 2.52 Digest::MD5
ok 2.84 File::Basename
ok 3.40 File::Spec::Functions
ok 0.23 File::Temp
ok 1.51 FindBin
ok 0.39 Font::TTF::Font
ok 2.71 GD
ok 0.2 GD::Polyline
ok 2.39 Getopt::Long
ok 1.16 IO::File
ok 0.33 List::MoreUtils
ok 1.38 List::Util
ok 0.01 Math::Bezier
ok 1.998 Math::BigFloat
ok 0.06 Math::Round
ok 0.08 Math::VecStat
ok 1.03 Memoize
ok 1.32 POSIX
ok 1.08 Params::Validate
ok 1.61 Pod::Usage
ok 2.05 Readonly
ok 2013031301 Regexp::Common
ok 2.84 SVG
ok 1.19 Set::IntSpan
ok 1.6611 Statistics::Basic
ok 2.41 Storable
ok 1.17 Sys::Hostname
ok 2.02 Text::Balanced
ok 0.61 Text::Format
ok 1.9725 Time::HiRes
See here for more info.
# use the perl CPAN shell
perl -MCPAN -e shell
## within the CPAN shell ##
# do for each module
install Config::General
By far the most annoying part of the installation… but at least there is a decent tutorial on compiling GD with all relevant libraries here.
cd ~/Applications/circos-0.69-9/example # or wherever you installed it
./run # will generate a logfile in /example/run.out
If everything looks good, you should see circos.svg and circos.png in circos-0.69-9/example, which appears at the top of this presentation.
# sample directory structure
tree ./circos_data
./circos_data
├── circos.png
├── circos.svg
├── data
│ ├── links.txt
│ ├── segments.txt
│ └── structure.label.txt
└── etc
├── bands.conf
├── circos.conf
├── color.brain.conf
├── heatmap.conf
├── ideogram.conf
├── ideogram.label.conf
├── ideogram.position.conf
├── segment.order.conf
├── text.rules.conf
└── ticks.conf
2 directories, 15 files
# run circos
cd ./circos_data
circos
debuggroup summary 0.10s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.018004
debuggroup summary 0.10s current working directory /Users/dmoracze/Desktop/coders_forum/2019_10/circos_data
debuggroup summary 0.10s command /Users/dmoracze/Applications/circos-0.69-9/bin/circos [no flags]
debuggroup summary 0.10s guessing configuration file
debuggroup summary 0.10s found conf file /Users/dmoracze/Desktop/coders_forum/2019_10/circos_data/etc/circos.conf
debuggroup summary 0.22s debug will appear for these features: output,summary
debuggroup summary 0.22s bitmap output image ./circos.png
debuggroup summary 0.22s SVG output image ./circos.svg
debuggroup summary 0.22s parsing karyotype and organizing ideograms
debuggroup summary 0.23s karyotype has 16 chromosomes of total size 12,800
debuggroup summary 0.24s applying global and local scaling
debuggroup summary 0.24s allocating image, colors and brushes
debuggroup summary 1.63s drawing 16 ideograms of total size 12,800
debuggroup summary 1.63s drawing highlights and ideograms
debuggroup summary 1.70s found conf file /Users/dmoracze/Applications/circos-0.69-9/bin/../etc/tracks/link.conf
debuggroup summary 1.71s found conf file /Users/dmoracze/Applications/circos-0.69-9/bin/../etc/tracks/link.conf
debuggroup summary 1.71s process track_0 link /Users/dmoracze/Desktop/coders_forum/2019_10/circos_data/data/links.txt
debuggroup summary 1.80s process track_1 link /Users/dmoracze/Desktop/coders_forum/2019_10/circos_data/data/links.txt
debuggroup summary 1.86s drawing link track_0 z 0
debuggroup summary 1.99s drawing link track_1 z 0
debuggroup summary 2.02s found conf file /Users/dmoracze/Applications/circos-0.69-9/bin/../etc/tracks/text.conf
debuggroup summary 2.02s processing track_0 text /Users/dmoracze/Desktop/coders_forum/2019_10/circos_data/data/structure.label.txt
debuggroup summary 2.05s drawing track_0 text z 0 structure.label.txt
debuggroup summary 2.05s placing text track data/structure.label.txt
debuggroup summary 2.05s ... see progress with -debug_group text
debuggroup summary 2.05s ... see placement summary with -debug_group textplace
debuggroup summary 2.16s found conf file /Users/dmoracze/Applications/circos-0.69-9/bin/../etc/tracks/axis.conf
debuggroup output 2.27s generating output
debuggroup output 2.62s created PNG image ./circos.png (1153 kb)
debuggroup output 2.62s created SVG image ./circos.svg (154 kb)
NB: if you run the circos command without flags, it will look in “logical” places for etc and data, however you can also manually provide the config file using -config filename.conf flag. By default it will write circos.png and circos.svg images to the directory from which the command was run, but this can also be changed using -outputdir and -outputfile flags.
For example:
My first Circos image (circa 2014)…